4AIM

Crystal structure of C. crescentus PNPase bound to RNase E recognition peptide

Summary for 4AIM

• Entry DOI: 10.2210/pdb4aim/pdb
• Related: 4AID
• Descriptor: POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE, RIBONUCLEASE, RNE/RNG FAMILY PROTEIN, PHOSPHATE ION, ... (4 entities in total)
• Functional Keywords: transferase-peptide complex, kh domain, s1 domain, gww peptide, transferase/peptide
• Biological source: CAULOBACTER VIBRIOIDES; More
• Cellular location: Cytoplasm (By similarity): Q9AC32
• Total number of polymer chains: 2
• Total formula weight: 80038.44

Authors

Hardwick, S.W.,Gubbey, T.,Hug, I.,Jenal, U.,Luisi, B.F. (deposition date: 2012-02-10, release date: 2012-04-18, Last modification date: 2023-12-20)

Primary citation

Hardwick, S.W.,Gubbey, T.,Hug, I.,Jenal, U.,Luisi, B.F.
Crystal Structure of Caulobacter Crescentus Polynucleotide Phosphorylase Reveals a Mechanism of RNA Substrate Channelling and RNA Degradosome Assembly.
Open Biol., 2:20028-, 2012

PubMed Abstract: Polynucleotide phosphorylase (PNPase) is an exoribonuclease that cleaves single-stranded RNA substrates with 3'-5' directionality and processive behaviour. Its ring-like, trimeric architecture creates a central channel where phosphorolytic active sites reside. One face of the ring is decorated with RNA-binding K-homology (KH) and S1 domains, but exactly how these domains help to direct the 3' end of single-stranded RNA substrates towards the active sites is an unsolved puzzle. Insight into this process is provided by our crystal structures of RNA-bound and apo Caulobacter crescentus PNPase. In the RNA-free form, the S1 domains adopt a 'splayed' conformation that may facilitate capture of RNA substrates. In the RNA-bound structure, the three KH domains collectively close upon the RNA and direct the 3' end towards a constricted aperture at the entrance of the central channel. The KH domains make non-equivalent interactions with the RNA, and there is a marked asymmetry within the catalytic core of the enzyme. On the basis of these data, we propose that structural non-equivalence, induced upon RNA binding, helps to channel substrate to the active sites through mechanical ratcheting. Structural and biochemical analyses also reveal the basis for PNPase association with RNase E in the multi-enzyme RNA degradosome assembly of the α-proteobacteria.

PubMed: 22724061
DOI: 10.1098/RSOB.120028

Experimental method

X-RAY DIFFRACTION (3.3 Å)